User:Wayne Decatur/UNH CME Workshop March 11 2011

Introduction

 * Overview of the workshop

Jmol

 * Jmol
 * The Application
 * The Java Applet - Demonstration
 * Advanced Options
 * Console
 * Works with small molecules too
 * Works with small molecules too and even can do energy minimization with them
 * Can be used to show chemical reactions
 * Compare Command Demonstration
 * 3D options - Demo with 3D ribosomal modifications maps database - Paint Your Own

Protein Data Bank

 * over 70,000 X-ray crystallography, NMR, and cryo-EM structures
 * about 85% are crystallographic structures
 * Metaphor with electron density
 * Caveat: Keep in mind these are models - Not all models or even portions of models created equally

Proteopedia

 * Proteopedia - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content
 * User or Sandbox login

Types of Proteopedia pages

 * Topic Pages
 * Macromolecular Structures
 * About Macromolecular Structure
 * PDB Entry Pages
 * User space Pages
 * Sandbox Pages
 * Workbench Pages
 * Interactive 3D Complements (I3DC) - Journal of Biological Inorganic Chemistry
 * Administrative
 * How To/Guides
 * Organizational/Table of Contents
 * Main Page - the main gateway

Topic Pages

 * Examples of structure pages
 * the ribosome structure; contrast with entry at PDB
 * Hemolysin
 * Quality toggle
 * Popup
 * Citrate Synthase
 * The Glutamate Receptor (GluA2)
 * Proteopedia pages can be exported for offline viewing using the toolbox on the left.
 * Information and Resource Collection, as well
 * About Macromolecular Structure
 * Cation-pi interactions
 * Searching

User Pages

 * Other users cannot edit pages in this space

PDB Entry Pages

 * Proteopedia has an entry for every PDB entry (over 70,000) with interactive scene links and links to useful resources
 * Example 1m10
 * Random Example: 1p3v (PDB 4 digit alphanumeric accession number)
 * Conservation:, explanation, and see also The ConSurf Database and The ConSurf Server Other examples: 4enl or 5cyt

FirstGlance in Jmol

 * Views and Convenience buttons
 * How many chains? - Use 3pla
 * Key Resources:
 * Biological Unit
 * Missing pieces?; PDBsum link on Proteopedia entry pages helpful for this as well

Assessing structure

 * Resolution noted with a link on each PDB entry page
 * Temperature factors, also see demonstration here
 * Gaps, i.e. missing pieces (see above)

Structural Biology for Non-structural Biologists

 * MolviZ "Top 5" by Eric Martz
 * Polyview-3D = fancy PyMol views and animations made super easy via a web server with forms.
 * Example - 3pla
 * Makes animations too and/or morphs too with multiple model structures

Proteopedia Page Authoring

 * Model of a wiki
 * Sandbox - there is a "student" login that can be used by groups for editing these for teaching purposes
 * Conveniences
 * Buttons for 3D structure windows and other commonly used items
 * Since a large amount of references are from Pub-Med, PMID all that is needed for references in text, combined with a reference list at end
 * Proteopedia:How to Make a Page
 * How to edit pages in Proteopedia
 * Special:Upload List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol

Proteopedia Scene Authoring

 * Proteopedia's Scene Authoring Tools
 * Load a structure 2zi0 or previous scene
 * Set your scene. Undo/Redo features.
 * Save your scene
 * Add the scene to the page
 * Try it out and then add and improve. Repeat.

Time permitting

 * Advanced scenes/toggles - MAKE EXAMPLE
 * Morphing allows displaying the visual transition between two molecular conformations.
 * Pymol to Jmol conversion built into Proteopedia's Scene Authoring Tools
 * Students at UMASS in classes associated with Chemistry-Biology Interface program design presentations for showing on the Molecular Playground
 * Jmol works with small molecules too
 * Works with small molecules too and even can do energy minimization with them
 * Can be used to show chemical reactions

Macromolecular Visualization

 * Eric Martz's recent workshop at his list of workshops.
 * Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman. Genome Biology 9:R121, August 2008 or doi:10.1186/gb-2008-9-8-r121
 * About Macromolecular Structure
 * FirstGlance in Jmol is very useful for exploring PDB entries or upload structure files.
 * Jmol Protein Explorer's powerful Quickviews approach really helps quickly generate useful views. This effort is building Chime-based Protein Explorer to work with Jmol, and a few features may still not yet work.
 * MolviZ "Top 5"
 * MolviZ.Org
 * Protein Explorer's Glossary
 * Jmol Application
 * PyMol
 * Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.
 * eMovie,a PyMol plug-in for macromolecular movie-making.

Small Molecule Visualization and Model Kits

 * CheMagic Virtual Molecular Model Kit
 * The Jmol Interface by Mike Evans at University of Illinois has a model kit interface and easy ways to arrows and items.
 * ChemCanvas, an open source chemical diagram editor
 * ChemTube3D has interactive animations and structures of molecules and reactions important in chemistry.

Topic Pages - Education

 * Teaching Strategies Using Proteopedia
 * Teaching Scenes, Tutorials, and Educators' Pages

Authoring Scenes and Views in Proteopedia and beyond

 * Proteopedia:Video Guide
 * Proteopedia:How to Make a Page
 * How to edit pages in Proteopedia ? Example 1, example 2, and example 3 of edited topic pages.
 * Special:Upload List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol
 * Proteopedia's Scene Authoring Tools
 * Perform basic editing and creation of scenes in your Sandboxes
 * Copying FirstGlance Scenes into Proteopedia


 * User:Tom Gluick/glutamine synthetase (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.
 * Jmol Command Reference Manual for advanced scene authoring in Jmol using commands because direct scripting works for Proteopedia too.
 * Comparison of Jmol tutorial-authoring systems
 * Copying FirstGlance in Jmol Scenes into Proteopedia
 * Jmol Protein Explorer's powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed here or at the JTAT site on extracting state scripts, it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be discrepancies and issues.
 * Jmol Tutorial-Authoring Template (JTAT) describes and works for developing and viewing scenes offline or developing and viewing privately.
 * Jmol Command Reference Manual for advanced scene authoring.
 * Jmol Wiki
 * Morphing allows displaying the visual transition between two molecular conformations.
 * Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.

Modeling

 * See the end of Eric Martz's recent workshop syllabus where he covers homology (more accurately, comparative) modeling.
 * A Feb. 1st 2011 news item about Yang Zhang and his work.
 * Mutating an amino acid in a proteins - here with PyMOL and here with Swiss PDB-Viewer
 * Homology modeling
 * Eric Martz's page on Homology Modeling
 * Swiss Model
 * Homology Models Database
 * Modbase -Database of Comparative Protein Structure Models
 * Comparative Modeling
 * Zhang Server (I-TASSER)
 * Ab Initio and Molecular Dynamics
 * Quark server
 * VMD - Visual Molecular Dynamics